This seems to be related to the Direct Rendering Infrastructure (DRI). By 
adding the line
  Option "DRI" "false"
to the "Device" section of /etc/X11/xorg.conf this went away when KMS was 
disabled (i.e running UMS). Alpha-2 has UMS by default, but the default has 
later been changed to KMS (see 
https://lists.ubuntu.com/archives/ubuntu-x/2009-June/000578.html). With KMS it 
happens no matter what (but AFAIK KMS is part of DRI, so it doesn't make sense 
to disable DRI with KMS enabled). Could you try the above line in xorg.conf and 
verify that the problem goes away then? You may also try KMS by either adding 
i915.modeset=1 at the LiveCD boot command line (F6 IIRC), or by trying a newer 
daily-live from http://cdimage.ubuntu.com/daily-live/ , but that may not be 
necessary.

I wanted to test with the VESA driver as well, but it didn't work at all
with KMS (reported as bug 401214), but with UMS and VESA it went away.

-- 
[i945] Displacement between Blender render window and content.
https://bugs.launchpad.net/bugs/400920
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